CCC Bug: Inconsistent cell type annotation - Githubissues

LieberInstitute / DLPFC_snRNAseq

snRNA_seq portion of the spatialDLPFC project

http://research.libd.org/spatialDLPFC/

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CCC Bug: Inconsistent cell type annotation #20

Closed boyiguo1 closed 2 years ago

boyiguo1 commented 2 years ago

Part of CCC analysis (#19)

Bug: Inconsistent var name for cellType annotation: We use cellType_hc != "drop" to drop cells, but use cellType_broad_hc as cell type annotation in LIANA https://github.com/boyiguo1/DLPFC_snRNAseq/blob/5d10ae022ccd577feee7f88230c604619a327511/Boyi_R/CCC_with_LIANA.R#L47 https://github.com/boyiguo1/DLPFC_snRNAseq/blob/5d10ae022ccd577feee7f88230c604619a327511/Boyi_R/CCC_with_LIANA.R#L71

TODO:

[ ] Use consistent cell type annotation in cell filtering and LIANA
[ ] Run LIANA again
- [x] Reduce the max mem for JHPCE to 20 GB ()

boyiguo1 commented 2 years ago

With further inspection, this is not a big deal.

The cellType_hc is the clustering including some subtypes of the broad type. Because our CCC analysis is on the broad type, and the drop are the same for both cellType_hc and cellType_broad_hc, we don't have to adjust anything